036e633e37ba018df11c2b2cb96c1dbd2eb46320 chmalee Thu Apr 20 12:12:09 2023 -0700 Restore a blank item name in the pcr results track, but stuff the primer pair name (which is now in the psls qName) into the map item name so clicks into hgc can still show the right primer details, refs #30925 diff --git src/hg/cgilib/pcrResult.c src/hg/cgilib/pcrResult.c index c927860..65b1148 100644 --- src/hg/cgilib/pcrResult.c +++ src/hg/cgilib/pcrResult.c @@ -1,214 +1,219 @@ /* pcrResult -- support for internal track of hgPcr results. */ /* Copyright (C) 2014 The Regents of the University of California * See kent/LICENSE or http://genome.ucsc.edu/license/ for licensing information. */ #include "common.h" #include "hdb.h" #include "hui.h" #include "obscure.h" #include "targetDb.h" #include "pcrResult.h" char *pcrResultCartVar(char *db) /* Returns the cart variable name for PCR result track info for db. * Don't free the result! */ { static char buf[1024]; safef(buf, sizeof(buf), "%s_%s", PCR_RESULT_TRACK_NAME, db); return buf; } #define setPtIfNotNull(pt, val) if (pt != NULL) *pt = val boolean pcrResultParseCart(char *db, struct cart *cart, char **retPslFile, char **retPrimerFile, struct targetDb **retTarget) /* Parse out hgPcrResult cart variable into components and make sure * they are valid. If so, set *ret's and return TRUE. Otherwise, null out * *ret's and return FALSE (and clear the cart variable if it exists). * ret's are ignored if NULL. */ { char *cartVar = pcrResultCartVar(cartString(cart, "db")); char *hgPcrResult = cartOptionalString(cart, cartVar); if (isEmpty(hgPcrResult)) { setPtIfNotNull(retPslFile, NULL); setPtIfNotNull(retPrimerFile, NULL); setPtIfNotNull(retTarget, NULL); return FALSE; } static char buf[2048]; char *words[3]; int wordCount; safecpy(buf, sizeof(buf), hgPcrResult); wordCount = chopLine(buf, words); if (wordCount < 2) errAbort("Badly formatted hgPcrResult variable: %s", hgPcrResult); char *pslFile = words[0]; char *primerFile = words[1]; char *targetName = (wordCount > 2) ? words[2] : NULL; struct targetDb *target = NULL; if (isNotEmpty(targetName)) target = targetDbLookup(db, targetName); if (!fileExists(pslFile) || !fileExists(primerFile) || (wordCount > 2 && target == NULL)) { cartRemove(cart, cartVar); setPtIfNotNull(retPslFile, NULL); setPtIfNotNull(retPrimerFile, NULL); setPtIfNotNull(retTarget, NULL); return FALSE; } setPtIfNotNull(retPslFile, cloneString(pslFile)); setPtIfNotNull(retPrimerFile, cloneString(primerFile)); setPtIfNotNull(retTarget, target); if (retTarget == NULL) targetDbFreeList(&target); return TRUE; } void pcrResultGetPrimers(char *fileName, char **retFPrimer, char **retRPrimer) /* Given a file whose first line is 2 words (forward primer, reverse primer) * set the ret's to upper-cased primer sequences. * Do not free the statically allocated ret's. */ { static char fPrimer[1024], rPrimer[1024];; struct lineFile *lf = lineFileOpen(fileName, TRUE); char *words[2]; if (! lineFileRow(lf, words)) lineFileAbort(lf, "Couldn't read primers"); if (retFPrimer != NULL) { safecpy(fPrimer, sizeof(fPrimer), words[0]); touppers(fPrimer); *retFPrimer = fPrimer; } if (retRPrimer != NULL) { safecpy(rPrimer, sizeof(rPrimer), words[1]); touppers(rPrimer); *retRPrimer = rPrimer; } lineFileClose(&lf); } void pcrResultGetPsl(char *fileName, struct targetDb *target, char *item, char *chrom, int itemStart, int itemEnd, struct psl **retItemPsl, struct psl **retOtherPsls) /* Read in psl from file. If a psl matches the given item position, set * retItemPsl to that; otherwise add it to retOtherPsls. Die if no psl * matches the given item position. */ { struct lineFile *lf = lineFileOpen(fileName, TRUE); struct psl *itemPsl = NULL, *otherPsls = NULL; char *pslFields[21]; while (lineFileRow(lf, pslFields)) { struct psl *psl = pslLoad(pslFields); boolean gotIt = FALSE; if (target != NULL) { if (sameString(psl->tName, item) && psl->tStart == itemStart && psl->tEnd == itemEnd) gotIt = TRUE; } else if (sameString(psl->tName, chrom) && psl->tStart == itemStart && psl->tEnd == itemEnd) gotIt = TRUE; if (gotIt) itemPsl = psl; else slAddHead(&otherPsls, psl); } lineFileClose(&lf); if (itemPsl == NULL) { if (target != NULL) errAbort("Did not find record for amplicon in %s sequence %s", target->description, item); else errAbort("Did not find record for amplicon at %s:%d-%d", chrom, itemStart, itemEnd); } if (retItemPsl != NULL) *retItemPsl = itemPsl; else pslFree(&itemPsl); if (retOtherPsls != NULL) { slSort(&otherPsls, pslCmpTarget); *retOtherPsls = otherPsls; } else pslFreeList(&otherPsls); } struct trackDb *pcrResultFakeTdb() /* Construct a trackDb record for PCR Results track. */ { struct trackDb *tdb; AllocVar(tdb); tdb->track = cloneString(PCR_RESULT_TRACK_NAME); tdb->table = cloneString(PCR_RESULT_TRACK_NAME); tdb->shortLabel = cloneString(PCR_RESULT_TRACK_LABEL); tdb->longLabel = cloneString(PCR_RESULT_TRACK_LONGLABEL); tdb->grp = cloneString("map"); tdb->type = cloneString("psl ."); tdb->priority = 100.01; tdb->canPack = TRUE; tdb->visibility = tvPack; tdb->html = hFileContentsOrWarning(hHelpFile(PCR_RESULT_TRACK_NAME)); trackDbPolish(tdb); if (tdb->settingsHash == NULL) tdb->settingsHash = hashNew(0); hashAdd(tdb->settingsHash, BASE_COLOR_DEFAULT, cloneString("diffBases")); hashAdd(tdb->settingsHash, BASE_COLOR_USE_SEQUENCE, cloneString(PCR_RESULT_TRACK_NAME)); hashAdd(tdb->settingsHash, SHOW_DIFF_BASES_ALL_SCALES, cloneString(".")); hashAdd(tdb->settingsHash, INDEL_DOUBLE_INSERT, cloneString("on")); hashAdd(tdb->settingsHash, INDEL_QUERY_INSERT, cloneString("on")); hashAdd(tdb->settingsHash, INDEL_POLY_A, cloneString("on")); hashAdd(tdb->settingsHash, "nextItemButton", cloneString("off")); return tdb; } -char *pcrResultItemAccName(char *acc, char *name) +char *pcrResultItemAccName(char *acc, char *name, struct psl *origPsl) /* If a display name is given in addition to the acc, concatenate them * into a single name that must match a non-genomic target item's name * in the targetDb .2bit. Do not free the result. */ { +if (origPsl) + return cloneString(origPsl->qName); +else + { static char accName[256]; if (isEmpty(name)) safecpy(accName, sizeof(accName), acc); else safef(accName, sizeof(accName), "%s__%s", acc, name); return accName; } +} char *pcrResultItemAccession(char *nameIn) /* If nameIn contains a concatenated accession and display name, returns * just the accession. Do not free the result.*/ { char *ptr = strstr(nameIn, "__"); if (ptr != NULL) { static char nameOut[128]; safecpy(nameOut, sizeof(nameOut), nameIn); nameOut[ptr-nameIn] = '\0'; return nameOut; } return nameIn; } char *pcrResultItemName(char *nameIn) /* If nameIn contains a concatenated accession and display name, returns * just the name. If accession only, returns NULL. Do not free the result.*/ { char *ptr = strstr(nameIn, "__"); if (ptr != NULL) return ptr+2; return NULL; }